--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Fri Nov 03 17:22:08 WET 2017
codeml.models=0 1 2 3 7 8
mrbayes.mpich=
mrbayes.ngen=1000000
tcoffee.alignMethod=CLUSTALW2
tcoffee.params=
tcoffee.maxSeqs=0
codeml.bin=codeml
mrbayes.tburnin=2500
codeml.dir=
input.sequences=
mrbayes.pburnin=2500
mrbayes.bin=mb_adops
tcoffee.bin=t_coffee_ADOPS
mrbayes.dir=/usr/bin/
tcoffee.dir=
tcoffee.minScore=3
input.fasta=
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/srevisao3/ClustalW2/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/srevisao3/ClustalW2/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p":
(Use the harmonic mean for Bayes factor comparisons of models)

(Values are saved to the file /opt/ADOPS1/srevisao3/ClustalW2/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -8620.95         -8642.28
2      -8622.46         -8640.30
--------------------------------------
TOTAL    -8621.44         -8641.71
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/srevisao3/ClustalW2/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/srevisao3/ClustalW2/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p":
Summaries are based on a total of 3002 samples from 2 runs.
Each run produced 2001 samples of which 1501 samples were included.
Parameter summaries saved to file "/opt/ADOPS1/srevisao3/ClustalW2/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         1.662669    0.003710    1.545015    1.779488    1.661510   1458.38   1479.69    1.000
r(A<->C){all}   0.117137    0.000123    0.094345    0.138212    0.116956    833.18    871.08    1.000
r(A<->G){all}   0.303239    0.000295    0.269569    0.335507    0.303244    650.14    680.13    1.000
r(A<->T){all}   0.077738    0.000048    0.065472    0.092078    0.077442    860.53   1017.00    1.002
r(C<->G){all}   0.153593    0.000196    0.126320    0.180436    0.153288    900.49    911.31    1.000
r(C<->T){all}   0.263002    0.000250    0.232186    0.294656    0.262471    701.74    743.14    1.000
r(G<->T){all}   0.085291    0.000073    0.067937    0.101739    0.085081    974.89   1039.56    1.001
pi(A){all}      0.294570    0.000115    0.274350    0.316345    0.294519    853.71    978.11    1.000
pi(C){all}      0.170549    0.000070    0.155259    0.187312    0.170326    736.60    778.84    1.000
pi(G){all}      0.194103    0.000076    0.177129    0.211534    0.194013    775.94    805.79    1.000
pi(T){all}      0.340777    0.000128    0.319727    0.363873    0.340775   1021.92   1085.50    1.000
alpha{1,2}      0.973170    0.017761    0.719502    1.225681    0.955347   1269.56   1278.29    1.000
alpha{3}        2.116155    0.209839    1.365843    3.040421    2.044388   1207.72   1317.74    1.000
pinvar{all}     0.028050    0.000572    0.000001    0.074940    0.021913   1133.52   1212.89    1.000
------------------------------------------------------------------------------------------------------
* Convergence diagnostic (ESS = Estimated Sample Size); min and avg values
correspond to minimal and average ESS among runs.
ESS value below 100 may indicate that the parameter is undersampled.
+ Convergence diagnostic (PSRF = Potential Scale Reduction Factor; Gelman
and Rubin, 1992) should approach 1.0 as runs converge.


Setting sumt conformat to Simple



 --- CODEML SUMMARY

Model 1: NearlyNeutral	-5546.008641
Model 2: PositiveSelection	-5506.94212
Model 0: one-ratio	-5690.898501
Model 3: discrete	-5506.465714
Model 7: beta	-5555.868136
Model 8: beta&w>1	-5510.055124


Model 0 vs 1	289.77971999999863

Model 2 vs 1	78.1330420000013

Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S28_SFBB1)

            Pr(w>1)     post mean +- SE for w

     5 N      0.998**       3.919
    11 R      0.998**       3.921
    15 P      0.950         3.780
    44 L      0.663         2.939
    51 E      0.998**       3.920
    64 A      0.910         3.663
    75 G      0.653         2.909
    99 I      0.998**       3.919
   101 T      1.000**       3.926
   162 E      0.721         3.111
   165 C      0.996**       3.914
   181 T      1.000**       3.926
   183 E      0.925         3.706

Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118)
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S28_SFBB1)

            Pr(w>1)     post mean +- SE for w

     5 N      0.997**       4.017 +- 0.576
    11 R      0.998**       4.020 +- 0.569
    15 P      0.929         3.795 +- 0.934
    44 L      0.596         2.732 +- 1.478
    51 E      0.998**       4.020 +- 0.570
    64 A      0.876         3.623 +- 1.109
    75 G      0.595         2.745 +- 1.495
    99 I      0.997**       4.018 +- 0.574
   101 T      1.000**       4.026 +- 0.553
   162 E      0.644         2.863 +- 1.443
   165 C      0.995**       4.012 +- 0.590
   181 T      1.000**       4.027 +- 0.550
   183 E      0.900         3.706 +- 1.039


Model 8 vs 7	91.62602399999923

Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S28_SFBB1)

            Pr(w>1)     post mean +- SE for w

     5 N      0.999**       3.448
    11 R      0.999**       3.449
    15 P      0.979*        3.396
    44 L      0.823         2.997
    51 E      0.999**       3.448
    53 G      0.537         2.255
    64 A      0.962*        3.354
    75 G      0.795         2.920
    91 R      0.659         2.576
    99 I      0.999**       3.448
   101 T      1.000**       3.451
   162 E      0.878         3.139
   165 C      0.998**       3.446
   181 T      1.000**       3.451
   183 E      0.965*        3.362

Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118)
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S28_SFBB1)

            Pr(w>1)     post mean +- SE for w

     5 N      0.999**       3.579 +- 0.320
    11 R      0.999**       3.580 +- 0.317
    15 P      0.967*        3.491 +- 0.563
    44 L      0.745         2.875 +- 1.184
    51 E      0.999**       3.579 +- 0.320
    64 A      0.942         3.422 +- 0.689
    75 G      0.722         2.813 +- 1.229
    91 R      0.544         2.321 +- 1.323
    99 I      0.998**       3.579 +- 0.321
   101 T      1.000**       3.583 +- 0.306
   162 E      0.807         3.041 +- 1.071
   165 C      0.997**       3.576 +- 0.334
   181 T      1.000**       3.583 +- 0.304
   183 E      0.949         3.442 +- 0.661